Latex Vorlage Dissertation Biologie

In this tutorial, I will explain howto write a thesis (which may be a master, PhD or any other thesis) using the document markup language LaTeX. I assume that most of you are using Windows as operating system, thus I did a fresh installation of Windows 8 and I will use it throughout this tutorial. Nevertheless, I think if you are using an older version of Windows, there might be no difference. For you guys using Mac Os X or Linux based systems, you may use the tutorial as well, but figure out howto install software components on your system by yourself. I am using Ubuntu and a MacBook, too, and will probably add some more tutorials for these systems soon. Ok, so we have a fresh raw installation of Windows 8, no additional software installed. Of course, before start writing anything for your thesis, you will have to get some fancy and helpful software. Here is an overview of software component that will be used throughout this tutorial where installation will be explained in the following sections.

MikTex (includes everything you need to run Latex)

Texmaker (Helpful editor to write Latex code)

Inkscape (Vector graphic program)

Dropbox (Save your work in the cloud)

Notepad++ (A great text editor)

Excel2Latex (Plugin to export tables from Excel to Latex)

Source files generated within this tutorial can be download here:Thesis Template

If you are a student of the faculty “Biologie und Vorklinische Medizin der Universität Regensburg” in Germany, you can also download the predefined title page:UR-TitlepageThesis Template with UR title page included

1. Install Software

1.1 Download and install MikTex

The first step is to download and install MiKTeX containing everything you need for working with LaTeX. Go to http://miktex.org/download and download the last available version. At the time of writing this post, the latest version is 2.9.4813. Fortunately, MiKTeX provides a nice installer. After downloading, simply start the installer and follow instructions. During installation, you will be asked for selecting your preferred paper size and for package installation:

If you live in Europe, you may select A4 as preferred paper size, Americans are using Letter as far as I know. So I usually choose A4. LaTeX is a software that has many additional stuff that can be added for specific things. For example, if you are a software developer, you might want to display source code of algorithms in your thesis. Therefore you want some additional functionality for LaTeX. Fortunately, there is a huge community providing stuff for anything you might imagine. These additional things are stored in so called packages. We will see later on how we can install and use them. MiKTeX is very nice to us by providing a package manager that is searching and installing packages for us. In the second option of the screenshot above, we can define if MiKTeX is allowed to install them on the fly, meaning if we are referencing a package in our code that is not yet installed, MiKTeX is recognizing it and installs it automatically. I prefer to be asked before, as I want to know which packages are being installed on my system. Remaining installation is just straight forward.

1.2 Download and install Texmaker

After we have successfully set up MiKTeX, we would be able to write some LaTeX code in any text editor and compile it using the command line. As not everyone writing in LaTeX is a nerd, we are about to use a special text editor (also called IDE for integrated development environment) that does some helpful things for us like syntax highlighting, auto completion and creating the final PDF file by only a mouse click. I prefer using Texmaker, which is freely available for all operation systems, but there are plenty of other excellent programs. If you are one of the Linux guys, you might also have a look at Kile. Go to http://www.xm1math.net/texmaker/download.html and download the latest version of Texmaker, I downloaded Texmaker 4.0.1 for Windows (texmakerwin32_install.exe). After downloading, start the installer and follow the instructions, it is straight forward. Next, start Texmaker, it should look like:

We immediately see that the program is built of three columns. Once we have started writing, the most left one will show the structure of our document, namely headings etc. The middle one is going to be our text editor where we put the LaTeX code in and the right one will show the translated PDF document. At this point I need to say, that we are going to translate our document into PDF. Originally, LaTeX is going to produce DVI files which is not used very often nowadays. Good, lets try if LaTeX already works by creating a new file by clicking the icon in the top left corner of Texmaker. Now, in the middle column, a new file has been opened. Type in the following and press save:

\documentclass{book} \begin{document} Test \end{document}

Please don’t worry what that means, we will revisit that later. If you are using Windows 8 as I do, you might wonder that you can’t save the file due to permission errors (Really Windows? Managed to have a new version that is even more silly than the old one?). The trick is that you have to provide a file extension on your own. So save the file as Test.tex not only Test. Note that .tex is the file extension indicating that this is a LaTeX file like .docx is used for Microsoft Word files.

On the bottom left of Texmaker, there are some buttons, press the Messages/Log button and you may note that at the bottom of the middle text editor column, something appeared called output window. This is a console that is providing output information of translating the text to the PDF file. Next, select from the top menu Tools->PDFLaTex and you will see that some messages are shown in the output window. Select Tools->PDFLaTex again. Next, select Tools->View PDF and a PDF file should be displayed in the right column of Texmaker:

Congratulations, you just created your first LaTeX document and successfully translated it to a PDF file. Please don’t worry about anything we’ve done so far, this was just to check whether our installation works or not. If you run into any trouble and you could not produce a PDF file, please check if your Texmaker has automatically identified LaTeX installation correctly. You may check that in Options->Configure Texmaker where Commands should look like:

Of course, some paths might be different.

Great, we are able to use LaTeX and can produce a PDF document from LaTeX code. But to write a fancy thesis, we need to install some more helpers.

1.3 Get Inkscape

Justifiably, you may ask: “Why do I need to install a graphics program? I just want to write my thesis and I already have plenty of graphic programs installed” OK, you do not necessarily need Inkscape, but you should use a software that can save images as vector graphics. Now, I may have finally confused you and you are angrily pressing your browsers back button know. I will clarify, there are generally speaking two kinds of images used on computers, the one and normally used ones are pixel based graphics, these are for example PNG or BMP or JPEG images like the screenshots provided in this tutorial. So, the image is built of a matrix of pixel values (squares) that do have one single color. You will have noticed that in the past while zooming an image too far. Further, there is the resolution, saying how many of these pixels exist in the image. The biggest disadvantage of this file formats is that if you are zooming the image, there are too less pixel values available and the image gets cloudy or you are seeing these pixel squares. Of course, we do not want to have cloudy images in our thesis, especially if we are providing graphs or similar stuff. The other option is to use vector graphics. A vector graphic image is simple a text file where the image is described in the sense of: “There is a black line of thickness 3 from the top left corner to the middle of the image”. The real painting of the image is done by the program that displays the image and if you zoom in, the lines, circles and whatever you may draw are still correctly defined. The end of this too long story is that we use vector graphics to get sharp images even if we zoom in extremely into the PDF file. Please note, that of course you cannot transform a pixel image or a photo into a vector graphic.

One of these programs you can create vector graphics with is Inkscape and it can be downloaded for free at http://inkscape.org/download/?lang=de. I have chosen the latest version 0.48.4. Once downloaded, just open the installer and click yourself through without any changes. We will revisit Inkscape later to learn how it is being used.

1.4 Even more software

Lastly, lets take some notes about other helpful software that you may use for writing your thesis.

First, I strongly recommend using any cloud drive service like Dropbox for saving your files into! Once you wrote the first 100 pages which took you probably a few month in real time and about 5 years of you age and your computer crashed for any weird reason you may be enormously happy to have a backup of your LaTeX code on a save place at the internet and you might even send me some flowers (I would prefer chocolate by the way) for giving you that hint. Further, I saved a version at the end of each day separately to be able to go back to any status of the thesis. A note for security and privacy folks, I agree with your complaints, but you can save your stuff encrypted or packed in a password saved zip file. Think about what is more critical, loosing all your work or having the risk of somebody hacking a cloud service seeing your LaTeX code?. Or make sure to save your stuff at least regularly on any independent hard drive.

Another helpful software, not only for your thesis, is called Notepad++ and is a text editor that serves anything you will need when editing text files. We will be using it later for managing our bibliography file.

Last but not least, I use Microsoft Excel to generate graphs, plots and tables as there is a nice wizard for changing styles etc. A huge advantage which I will also explain in one of the next parts of this tutorial is that you can export graphics from Excel to PDF as vector graphics. As you remember, this leads to graphs that can be scaled to any extreme. An excellent plug-in for Excel is Excel2Latex. You will only have to download the file from the website and open it with Excel to get two additional buttons in your Excel Add-Ins menu. You can find additional information on installation at the project website.

Conclusion

In Part 1 of this tutorial, we managed to set up our system to be able to start writing our thesis and we already produced a little PDF document using LaTeX. Part 2 is going to quickly introduce LaTeX. There are plenty of more extended and better introductions to really learn how to deal with LaTeX. But I want to give a short overview of what it is and why it makes sense to use it. But you will learn how to organize your folders, files and how to build the general structure of your thesis

The most interesting part will probably be Part 3, where I gonna show you some of the hacks and tricks that I have used to make life easier and to produce a nice looking thesis (at least in my opinion).

==> Continue with Part 2

This entry was posted in Latex and tagged Excel2Latex, Inkscape, Latex, Miktex, Notepad++, TexMaker, Thesis by Torsten. Bookmark the permalink.